What is CNV detection?
CNVs are the genetic cause of multiple hereditary diseases [2]. To detect them, specific tools and techniques are required. In genetic diagnostics, this is mainly done using either MLPA and aCGH or using software tools to infer copy-number alterations from NGS data generated in the diagnostics process.
How is CNV calculated?
The CNV is simply given by the ratio of the estimated concentration of the target gene to the estimated concentration of the reference gene. Both of these concentrations are estimated by applying the Poisson law as explained in the item Poisson Law Computation.
What is NGS CNV analysis?
NGS-Based Copy Number Analysis By providing a base-by-base view of the genome, NGS detects small or novel copy number variants that arrays often miss. NGS can also map the exact location of a CNV. The high resolution of sequencing complements the high throughput of arrays, enabling a comprehensive view of the genome.
How can duplications arise?
Duplications arise from an event termed unequal crossing-over that occurs during meiosis between misaligned homologous chromosomes. The chance of it happening is a function of the degree of sharing of repetitive elements between two chromosomes.
Is CNV the same as macular degeneration?
Choroidal neovascularization (CNV) is the medical term for growth of new blood vessels beneath the eye’s retina (subretinal). It can be painless, but can lead to macular degeneration, a major cause of vision loss. This condition may respond to treatment, while being incurable.
How do you detect CNVs?
2.1 Classical methods used to detect CNVs Since the advent of genetic testing in clinical laboratories, various techniques have been introduced to detect CNVs. Comparative Genomic Hybridization (CGH) was one of the earliest techniques used to detect genome-wide CNVs (CNVs spread throughout the genome).
Which CNV scanner is the best for detecting rare CNVs?
When detecting rare CNVs, ExomeDepth showed the highest sensitivity and CONIFER showed the lowest false positive rate cnvScan can be used effectively to reduce false positive counts based on CNV quality scores
Are there tools for CNVs detection from NGS data?
Many tools for CNVs detection from NGS data have been developed. Most of them can reliably call large CNVs (in the order of megabases) but show poor performance when dealing with small CNVs affecting only one or a few small exons, which are CNVs frequently involved in several genetic diseases.
What are the gold standards for CNV detection in genetic diagnostics?
The gold standards for CNV detection in genetic diagnostics are multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (aCGH) [ 3, 4 ].